The Angel and The Boot and Shoe, both in Ackworth, near Wakefield in West Yorkshire, both shut their doors on Thursday.
It comes only two days after four other pubs closed when customers tested positive just hours after reopening.
Pubs, bars and restaurants in England were allowed to reopen last weekend on what was dubbed "Super Saturday" following 104 days of lockdown, with strict hygiene and social distancing measures in force.
Hundreds welcomed back customers but crowds in London, Nottinghamshire and in Market Harborough, on the edge of Leicester — which remains in local lockdown after a cases surge — sparked fears of a second wave.
On Thursday, The Angel posted on Facebook: “We will be closed today 9/7/20 to deep clean after a customer has informed us they have tested positive for Coronavirus. This customer visited us on Saturday evening between 8pm and 10pm.
“We have been in contact with all staff members to make sure they are safe and are not showing any symptoms and have advised them on what to do if they are.
“We apologise if anyone has a booking with us and we hope to see you in the near future.”
Less than an hour later, the Boot and Shoe said in a statement: “Due to a customer, who visited the Boot & Shoe on Saturday afternoon, testing positive for Covid-19 we will be closed today (Thursday 9th July) to carry out a full deep clean and sanitisation.
“We are currently working with NHS Track & Trace to contact all customers who visited on Saturday 4th July.
“All our staff have been tested for the virus today and we will hopefully reopen tomorrow at 4pm. Thank you for your assistance and support.”
On Tuesday, the Lighthouse Kitchen and Carvery in Burnham-on-Sea, Somerset, said it was “slowly” combing the list of customers’ details it had collected after one tested positive.
Jess Green, the landlady, rang at least 90 people who had left their contact details during their visit on Saturday but all staff had tested negative.
Calling it “stressful”, she told BBC Radio 4’s World At One programme: “The main thing that was going through our heads was we had to make sure everyone was safe, that we contacted every one of our customers.
“We took it upon ourselves, because obviously test and trace can do all that, but we took it upon ourselves to do it because we knew that we had done it before it got out there.”
We will be closed today 9/7/20 to deep clean after a customer has informed us they have tested positive for Coronavirus....Posted byThe AngelonThursday, July 9, 2020
The same day in Batley, West Yorkshire, the Fox and Hounds said a customer had phoned to say they had tested positive for coronavirus.
The landlord of the Village Home Pub in Alverstoke, Hampshire, said on Tuesday that his team were awaiting test results after someone in a member of staff's "family bubble" tested positive.
Customer Announcement.... Due to a customer, who visited the Boot & Shoe on Saturday afternoon, testing positive for...Posted byBoot & Shoe, AckworthonThursday, July 9, 2020
The Fighting Cocks, a second pub in the Alverstoke area of Gosport, closed its doors after the confirmed case from the Village Home as a precaution.
Praising landlords for choosing to shut, Mr Hancock told MPs earlier this week that they were “doing the right thing by their customers and by their communities”.
“This is NHS Test and Trace working precisely as intended,” he said. “Three pubs shut so that others can be open.”